Introduction To use biomarkers in monitoring programmes, potential confounding factors must be considered. In the clam Scrobicularia plana, the influence of size and salinity on biomarkers at different levels of biological organisation has been examined. Materials and methods Biochemical (glutathione-S-transferase, lactate dehydrogenase, acetylcholinesterase, digestive enzymes, metallothionein), physiological (energy reserves) and behavioural (burrowing) responses were compared (a) in specimens of different sizes from the Loire estuary; (b) in specimens from the Belon estuary at two sites with salinities of 30.1 or 11.5. Results Amongst the biomarkers able to reveal pollution effects, several are influenced by the size of the clams (Ag, Cu, Ni and glycogen concentrations, GST and AChE activities, condition indices). Salinity differences induced variations of the same order of magnitude (GST, AChE) or even higher (lactate dehydrogenase, digestive enzymes in the crystalline style) than contamination-induced variations. In burrowing tests, the number of burrowed specimens was similar at both salinities after an experiment time < 3 h. Conclusions Size is a factor necessarily but easily controlled. Because the weight may be different in clams of identical size, correction factors may be used to minimise the influence of weight changes on biomarkers. A correction factor taking into account salinity levels can also be used. The protein concentrations in the clams did not differ with salinity, a very favourable outcome since all enzyme activities are classically expressed by reference to total protein concentrations. For burrowing tests, the number of burrowed specimens at a particular time is an endpoint that is preferable to measures of burrowing speed.